Fix tests: Synonym Sync

[joeflack4]

Overview

Due to some refactoring these tests are failing.

Details

/Users/joeflack4/virtualenvs/mondo-ingest/bin/python /Applications/PyCharm.app/Contents/plugins/python/helpers/pydev/[pydevd.py](http://pydevd.py/) --multiprocess --qt-support=auto --client 127.0.0.1 --port 55914 --file /Applications/PyCharm.app/Contents/plugins/python/helpers/pycharm/_jb_pytest_runner.py --path /Users/joeflack4/projects/mondo-ingest/tests/[test_sync_synonym.py](http://test_sync_synonym.py/) 
Testing started at 4:09 PM ...
Connected to pydev debugger (build 233.15325.20)
Launching pytest with arguments /Users/joeflack4/projects/mondo-ingest/tests/[test_sync_synonym.py](http://test_sync_synonym.py/) --no-header --no-summary -q in /Users/joeflack4/projects/mondo-ingest/tests

============================= test session starts ==============================
collecting ... collected 4 items

[test_sync_synonym.py](http://test_sync_synonym.py/)::TestSyncSynonyms::test_added 
[test_sync_synonym.py](http://test_sync_synonym.py/)::TestSyncSynonyms::test_confirmed 
[test_sync_synonym.py](http://test_sync_synonym.py/)::TestSyncSynonyms::test_deleted 
[test_sync_synonym.py](http://test_sync_synonym.py/)::TestSyncSynonyms::test_updated 

======================== 3 warnings, 4 errors in 3.44s =========================
ERROR                 [ 25%]
test setup failed
cls = <class 'test_sync_synonym.TestSyncSynonyms'>

    @classmethod
    def setUpClass(cls):
        """Set up"""
        # todo: #1 run pipeline / prereqs - dependent on fixing _run_make_goal()
        # if not os.path.exists(INPUT_SOURCE_DB):
        #     cls._run_make_goal('../../tests/input/sync_synonym/omim.db')
        # if not os.path.exists(INPUT_MONDO_DB):
        #     cls._run_make_goal('../../tests/input/sync_synonym/mondo.db')
        # if not os.path.exists(INPUT_MONDO_SYNONYMS):
        #     cls._run_make_goal('../../tests/input/sync_synonym/mondo-synonyms-scope-type-xref.tsv')
>       sync_synonyms(
            ontology_db_path=INPUT_SOURCE_DB,
            mondo_synonyms_path=INPUT_MONDO_SYNONYMS,
            mondo_exclusion_configs=INPUT_EXCLUDED_SYNONYMS,
            mondo_mappings_path=INPUT_MAPPINGS,
            onto_synonym_types_path=INPUT_ONTO_SYNONYMS,
            onto_config_path=INPUT_SOURCE_METADATA,
            outpath_added=OUTPUT_ADDED,
            outpath_confirmed=OUTPUT_CONFIRMED,
            # outpath_deleted=OUTPUT_DELETED,
            outpath_updated=OUTPUT_UPDATED,
            combined_outpath_template_str=None
        )

[test_sync_synonym.py](http://test_sync_synonym.py/):77: 
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 

ontology_db_path = PosixPath('/Users/joeflack4/projects/mondo-ingest/tests/input/sync_synonym/test_omim.db')
mondo_synonyms_path = PosixPath('/Users/joeflack4/projects/mondo-ingest/tests/input/sync_synonym/mondo-synonyms-scope-type-xref.tsv')
mondo_exclusion_configs = PosixPath('/Users/joeflack4/projects/mondo-ingest/src/ontology/config/mondo-excluded-values.yml')
onto_synonym_types_path = PosixPath('/Users/joeflack4/projects/mondo-ingest/tests/input/sync_synonym/omim-synonyms-scope-type-xref.tsv')
mondo_mappings_path = PosixPath('/Users/joeflack4/projects/mondo-ingest/tests/input/sync_synonym/test_mondo.sssom.tsv')
onto_config_path = PosixPath('/Users/joeflack4/projects/mondo-ingest/src/ontology/metadata/omim.yml')
outpath_added = PosixPath('/Users/joeflack4/projects/mondo-ingest/tests/output/omim.synonyms.added.robot.tsv')
outpath_confirmed = PosixPath('/Users/joeflack4/projects/mondo-ingest/tests/output/omim.synonyms.confirmed.robot.tsv')
outpath_updated = PosixPath('/Users/joeflack4/projects/mondo-ingest/tests/output/omim.synonyms.updated.robot.tsv')
outpath_deleted = None, combined_outpath_template_str = None

    def sync_synonyms(
        ontology_db_path: Union[Path, str], mondo_synonyms_path: Union[Path, str],
        mondo_exclusion_configs: Union[Path, str], onto_synonym_types_path: Union[Path, str],
        mondo_mappings_path: Union[Path, str], onto_config_path: Union[Path, str], outpath_added: Union[Path, str],
        outpath_confirmed: Union[Path, str], outpath_updated: Union[Path, str], outpath_deleted: Union[Path, str] = None,
        combined_outpath_template_str='tmp/synonym_sync_combined_cases_{}.tsv'
    ):
        """Create outputs for syncing synonyms between Mondo and its sources.
    
        todo: update when -deleted is reactivated
        :param outpath_deleted: Optional. This case isn't fully fleshed out yet.
    
        todo: if we decided that this param should stay, set as required CLI/functional param w/ no default value.
        :param combined_outpath_template_str: Creates an additional file concatenating all case files.
    
        todo: possible refactor: labels: Maybe could be done more cleanly and consistently. At first, wanted to add to both
         source_df and mondo_df, but this caused _x and _y cols during joins, or I would have to join on those cols as well.
         So I arbitrarily chose mondo_df. This is fine in all cases but -added, where they're added in a custom way.
        """
        # Read configurations
>       with open(mondo_exclusion_configs, 'r') as stream:
E       FileNotFoundError: [Errno 2] No such file or directory: '/Users/joeflack4/projects/mondo-ingest/src/ontology/config/mondo-excluded-values.yml'

../src/scripts/[sync_synonym.py](http://sync_synonym.py/):223: FileNotFoundError
ERROR             [ 50%]
test setup failed
cls = <class 'test_sync_synonym.TestSyncSynonyms'>

    @classmethod
    def setUpClass(cls):
        """Set up"""
        # todo: #1 run pipeline / prereqs - dependent on fixing _run_make_goal()
        # if not os.path.exists(INPUT_SOURCE_DB):
        #     cls._run_make_goal('../../tests/input/sync_synonym/omim.db')
        # if not os.path.exists(INPUT_MONDO_DB):
        #     cls._run_make_goal('../../tests/input/sync_synonym/mondo.db')
        # if not os.path.exists(INPUT_MONDO_SYNONYMS):
        #     cls._run_make_goal('../../tests/input/sync_synonym/mondo-synonyms-scope-type-xref.tsv')
>       sync_synonyms(
            ontology_db_path=INPUT_SOURCE_DB,
            mondo_synonyms_path=INPUT_MONDO_SYNONYMS,
            mondo_exclusion_configs=INPUT_EXCLUDED_SYNONYMS,
            mondo_mappings_path=INPUT_MAPPINGS,
            onto_synonym_types_path=INPUT_ONTO_SYNONYMS,
            onto_config_path=INPUT_SOURCE_METADATA,
            outpath_added=OUTPUT_ADDED,
            outpath_confirmed=OUTPUT_CONFIRMED,
            # outpath_deleted=OUTPUT_DELETED,
            outpath_updated=OUTPUT_UPDATED,
            combined_outpath_template_str=None
        )

[test_sync_synonym.py](http://test_sync_synonym.py/):77: 
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 

ontology_db_path = PosixPath('/Users/joeflack4/projects/mondo-ingest/tests/input/sync_synonym/test_omim.db')
mondo_synonyms_path = PosixPath('/Users/joeflack4/projects/mondo-ingest/tests/input/sync_synonym/mondo-synonyms-scope-type-xref.tsv')
mondo_exclusion_configs = PosixPath('/Users/joeflack4/projects/mondo-ingest/src/ontology/config/mondo-excluded-values.yml')
onto_synonym_types_path = PosixPath('/Users/joeflack4/projects/mondo-ingest/tests/input/sync_synonym/omim-synonyms-scope-type-xref.tsv')
mondo_mappings_path = PosixPath('/Users/joeflack4/projects/mondo-ingest/tests/input/sync_synonym/test_mondo.sssom.tsv')
onto_config_path = PosixPath('/Users/joeflack4/projects/mondo-ingest/src/ontology/metadata/omim.yml')
outpath_added = PosixPath('/Users/joeflack4/projects/mondo-ingest/tests/output/omim.synonyms.added.robot.tsv')
outpath_confirmed = PosixPath('/Users/joeflack4/projects/mondo-ingest/tests/output/omim.synonyms.confirmed.robot.tsv')
outpath_updated = PosixPath('/Users/joeflack4/projects/mondo-ingest/tests/output/omim.synonyms.updated.robot.tsv')
outpath_deleted = None, combined_outpath_template_str = None

    def sync_synonyms(
        ontology_db_path: Union[Path, str], mondo_synonyms_path: Union[Path, str],
        mondo_exclusion_configs: Union[Path, str], onto_synonym_types_path: Union[Path, str],
        mondo_mappings_path: Union[Path, str], onto_config_path: Union[Path, str], outpath_added: Union[Path, str],
        outpath_confirmed: Union[Path, str], outpath_updated: Union[Path, str], outpath_deleted: Union[Path, str] = None,
        combined_outpath_template_str='tmp/synonym_sync_combined_cases_{}.tsv'
    ):
        """Create outputs for syncing synonyms between Mondo and its sources.
    
        todo: update when -deleted is reactivated
        :param outpath_deleted: Optional. This case isn't fully fleshed out yet.
    
        todo: if we decided that this param should stay, set as required CLI/functional param w/ no default value.
        :param combined_outpath_template_str: Creates an additional file concatenating all case files.
    
        todo: possible refactor: labels: Maybe could be done more cleanly and consistently. At first, wanted to add to both
         source_df and mondo_df, but this caused _x and _y cols during joins, or I would have to join on those cols as well.
         So I arbitrarily chose mondo_df. This is fine in all cases but -added, where they're added in a custom way.
        """
        # Read configurations
>       with open(mondo_exclusion_configs, 'r') as stream:
E       FileNotFoundError: [Errno 2] No such file or directory: '/Users/joeflack4/projects/mondo-ingest/src/ontology/config/mondo-excluded-values.yml'

../src/scripts/[sync_synonym.py](http://sync_synonym.py/):223: FileNotFoundError
ERROR               [ 75%]
test setup failed
cls = <class 'test_sync_synonym.TestSyncSynonyms'>

    @classmethod
    def setUpClass(cls):
        """Set up"""
        # todo: #1 run pipeline / prereqs - dependent on fixing _run_make_goal()
        # if not os.path.exists(INPUT_SOURCE_DB):
        #     cls._run_make_goal('../../tests/input/sync_synonym/omim.db')
        # if not os.path.exists(INPUT_MONDO_DB):
        #     cls._run_make_goal('../../tests/input/sync_synonym/mondo.db')
        # if not os.path.exists(INPUT_MONDO_SYNONYMS):
        #     cls._run_make_goal('../../tests/input/sync_synonym/mondo-synonyms-scope-type-xref.tsv')
>       sync_synonyms(
            ontology_db_path=INPUT_SOURCE_DB,
            mondo_synonyms_path=INPUT_MONDO_SYNONYMS,
            mondo_exclusion_configs=INPUT_EXCLUDED_SYNONYMS,
            mondo_mappings_path=INPUT_MAPPINGS,
            onto_synonym_types_path=INPUT_ONTO_SYNONYMS,
            onto_config_path=INPUT_SOURCE_METADATA,
            outpath_added=OUTPUT_ADDED,
            outpath_confirmed=OUTPUT_CONFIRMED,
            # outpath_deleted=OUTPUT_DELETED,
            outpath_updated=OUTPUT_UPDATED,
            combined_outpath_template_str=None
        )

[test_sync_synonym.py](http://test_sync_synonym.py/):77: 
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 

ontology_db_path = PosixPath('/Users/joeflack4/projects/mondo-ingest/tests/input/sync_synonym/test_omim.db')
mondo_synonyms_path = PosixPath('/Users/joeflack4/projects/mondo-ingest/tests/input/sync_synonym/mondo-synonyms-scope-type-xref.tsv')
mondo_exclusion_configs = PosixPath('/Users/joeflack4/projects/mondo-ingest/src/ontology/config/mondo-excluded-values.yml')
onto_synonym_types_path = PosixPath('/Users/joeflack4/projects/mondo-ingest/tests/input/sync_synonym/omim-synonyms-scope-type-xref.tsv')
mondo_mappings_path = PosixPath('/Users/joeflack4/projects/mondo-ingest/tests/input/sync_synonym/test_mondo.sssom.tsv')
onto_config_path = PosixPath('/Users/joeflack4/projects/mondo-ingest/src/ontology/metadata/omim.yml')
outpath_added = PosixPath('/Users/joeflack4/projects/mondo-ingest/tests/output/omim.synonyms.added.robot.tsv')
outpath_confirmed = PosixPath('/Users/joeflack4/projects/mondo-ingest/tests/output/omim.synonyms.confirmed.robot.tsv')
outpath_updated = PosixPath('/Users/joeflack4/projects/mondo-ingest/tests/output/omim.synonyms.updated.robot.tsv')
outpath_deleted = None, combined_outpath_template_str = None

    def sync_synonyms(
        ontology_db_path: Union[Path, str], mondo_synonyms_path: Union[Path, str],
        mondo_exclusion_configs: Union[Path, str], onto_synonym_types_path: Union[Path, str],
        mondo_mappings_path: Union[Path, str], onto_config_path: Union[Path, str], outpath_added: Union[Path, str],
        outpath_confirmed: Union[Path, str], outpath_updated: Union[Path, str], outpath_deleted: Union[Path, str] = None,
        combined_outpath_template_str='tmp/synonym_sync_combined_cases_{}.tsv'
    ):
        """Create outputs for syncing synonyms between Mondo and its sources.
    
        todo: update when -deleted is reactivated
        :param outpath_deleted: Optional. This case isn't fully fleshed out yet.
    
        todo: if we decided that this param should stay, set as required CLI/functional param w/ no default value.
        :param combined_outpath_template_str: Creates an additional file concatenating all case files.
    
        todo: possible refactor: labels: Maybe could be done more cleanly and consistently. At first, wanted to add to both
         source_df and mondo_df, but this caused _x and _y cols during joins, or I would have to join on those cols as well.
         So I arbitrarily chose mondo_df. This is fine in all cases but -added, where they're added in a custom way.
        """
        # Read configurations
>       with open(mondo_exclusion_configs, 'r') as stream:
E       FileNotFoundError: [Errno 2] No such file or directory: '/Users/joeflack4/projects/mondo-ingest/src/ontology/config/mondo-excluded-values.yml'

../src/scripts/[sync_synonym.py](http://sync_synonym.py/):223: FileNotFoundError
ERROR               [100%]
test setup failed
cls = <class 'test_sync_synonym.TestSyncSynonyms'>

    @classmethod
    def setUpClass(cls):
        """Set up"""
        # todo: #1 run pipeline / prereqs - dependent on fixing _run_make_goal()
        # if not os.path.exists(INPUT_SOURCE_DB):
        #     cls._run_make_goal('../../tests/input/sync_synonym/omim.db')
        # if not os.path.exists(INPUT_MONDO_DB):
        #     cls._run_make_goal('../../tests/input/sync_synonym/mondo.db')
        # if not os.path.exists(INPUT_MONDO_SYNONYMS):
        #     cls._run_make_goal('../../tests/input/sync_synonym/mondo-synonyms-scope-type-xref.tsv')
>       sync_synonyms(
            ontology_db_path=INPUT_SOURCE_DB,
            mondo_synonyms_path=INPUT_MONDO_SYNONYMS,
            mondo_exclusion_configs=INPUT_EXCLUDED_SYNONYMS,
            mondo_mappings_path=INPUT_MAPPINGS,
            onto_synonym_types_path=INPUT_ONTO_SYNONYMS,
            onto_config_path=INPUT_SOURCE_METADATA,
            outpath_added=OUTPUT_ADDED,
            outpath_confirmed=OUTPUT_CONFIRMED,
            # outpath_deleted=OUTPUT_DELETED,
            outpath_updated=OUTPUT_UPDATED,
            combined_outpath_template_str=None
        )

[test_sync_synonym.py](http://test_sync_synonym.py/):77: 
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 

ontology_db_path = PosixPath('/Users/joeflack4/projects/mondo-ingest/tests/input/sync_synonym/test_omim.db')
mondo_synonyms_path = PosixPath('/Users/joeflack4/projects/mondo-ingest/tests/input/sync_synonym/mondo-synonyms-scope-type-xref.tsv')
mondo_exclusion_configs = PosixPath('/Users/joeflack4/projects/mondo-ingest/src/ontology/config/mondo-excluded-values.yml')
onto_synonym_types_path = PosixPath('/Users/joeflack4/projects/mondo-ingest/tests/input/sync_synonym/omim-synonyms-scope-type-xref.tsv')
mondo_mappings_path = PosixPath('/Users/joeflack4/projects/mondo-ingest/tests/input/sync_synonym/test_mondo.sssom.tsv')
onto_config_path = PosixPath('/Users/joeflack4/projects/mondo-ingest/src/ontology/metadata/omim.yml')
outpath_added = PosixPath('/Users/joeflack4/projects/mondo-ingest/tests/output/omim.synonyms.added.robot.tsv')
outpath_confirmed = PosixPath('/Users/joeflack4/projects/mondo-ingest/tests/output/omim.synonyms.confirmed.robot.tsv')
outpath_updated = PosixPath('/Users/joeflack4/projects/mondo-ingest/tests/output/omim.synonyms.updated.robot.tsv')
outpath_deleted = None, combined_outpath_template_str = None

    def sync_synonyms(
        ontology_db_path: Union[Path, str], mondo_synonyms_path: Union[Path, str],
        mondo_exclusion_configs: Union[Path, str], onto_synonym_types_path: Union[Path, str],
        mondo_mappings_path: Union[Path, str], onto_config_path: Union[Path, str], outpath_added: Union[Path, str],
        outpath_confirmed: Union[Path, str], outpath_updated: Union[Path, str], outpath_deleted: Union[Path, str] = None,
        combined_outpath_template_str='tmp/synonym_sync_combined_cases_{}.tsv'
    ):
        """Create outputs for syncing synonyms between Mondo and its sources.
    
        todo: update when -deleted is reactivated
        :param outpath_deleted: Optional. This case isn't fully fleshed out yet.
    
        todo: if we decided that this param should stay, set as required CLI/functional param w/ no default value.
        :param combined_outpath_template_str: Creates an additional file concatenating all case files.
    
        todo: possible refactor: labels: Maybe could be done more cleanly and consistently. At first, wanted to add to both
         source_df and mondo_df, but this caused _x and _y cols during joins, or I would have to join on those cols as well.
         So I arbitrarily chose mondo_df. This is fine in all cases but -added, where they're added in a custom way.
        """
        # Read configurations
>       with open(mondo_exclusion_configs, 'r') as stream:
E       FileNotFoundError: [Errno 2] No such file or directory: '/Users/joeflack4/projects/mondo-ingest/src/ontology/config/mondo-excluded-values.yml'

../src/scripts/[sync_synonym.py](http://sync_synonym.py/):223: FileNotFoundError

Process finished with exit code 1